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commit: 9476c6092f42b86735e48bce06762cff70b14869 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Mon Nov 12 15:54:13 2018 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Mon Nov 12 15:54:13 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9476c609 |
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|
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sci-chemistry/gromacs: Version bump |
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|
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Package-Manager: Portage-2.3.51, Repoman-2.3.12 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 2 + |
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sci-chemistry/gromacs/gromacs-2018.3-r1.ebuild | 270 +++++++++++++++++++++++++ |
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sci-chemistry/gromacs/gromacs-2018.4.ebuild | 270 +++++++++++++++++++++++++ |
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3 files changed, 542 insertions(+) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index eafd2138713..3a34577c4bd 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,12 +1,14 @@ |
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DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 |
24 |
DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 |
25 |
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f |
26 |
+DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955 |
27 |
DIST gromacs-2019-beta1.tar.gz 33549950 BLAKE2B 667246f9a7cb136efca3fbda21aabe5ab0a759aa42896f8a9ddc86fafbfb1906e31fe46688c98477a5841e8fe5708b960c2a26abe754b8d793046734cd509377 SHA512 9f8bec3671f6f7421dc45cab1b5edb8ba8f2ebc34cd19ebd3d5d534be1f84135a112f49733a3f8c79e93ffc2b09c5053ae0dea31e95832a2b98acaee47f7d1af |
28 |
DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee |
29 |
DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 |
30 |
DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 |
31 |
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff |
32 |
DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b |
33 |
+DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe |
34 |
DIST regressiontests-2019-beta1.tar.gz 67604794 BLAKE2B 163046e54206d3406d39e6bd9552dcce5a9a05a73e14249bf371d2432d902a3e336c0caa3e0c83353ac4566d91f4f805724f8eb996a831f8d3b712f65b1d1c42 SHA512 eef7eaacf56ba9358bfb0a3e34da4bc00d2a65564da81d144f57ee8a732081882b8e1c96f7006b966455105b834271715273e7590d3d4310209ee0324e7fa585 |
35 |
DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 |
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DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2018.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2018.3-r1.ebuild |
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new file mode 100644 |
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index 00000000000..485db2a26ac |
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--- /dev/null |
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+++ b/sci-chemistry/gromacs/gromacs-2018.3-r1.ebuild |
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@@ -0,0 +1,270 @@ |
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+# Copyright 1999-2018 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+CMAKE_MAKEFILE_GENERATOR="ninja" |
50 |
+ |
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+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
52 |
+ |
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+if [[ $PV = *9999* ]]; then |
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+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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+ https://gerrit.gromacs.org/gromacs.git |
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+ https://github.com/gromacs/gromacs.git |
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+ http://repo.or.cz/r/gromacs.git" |
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+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
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+ inherit git-r3 |
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+else |
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+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
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+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
64 |
+fi |
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+ |
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+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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+ |
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+DESCRIPTION="The ultimate molecular dynamics simulation package" |
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+HOMEPAGE="http://www.gromacs.org/" |
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+ |
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+# see COPYING for details |
72 |
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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+SLOT="0/${PV}" |
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+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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+ |
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+CDEPEND=" |
79 |
+ X? ( |
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+ x11-libs/libX11 |
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+ x11-libs/libSM |
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+ x11-libs/libICE |
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+ ) |
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+ blas? ( virtual/blas ) |
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+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
86 |
+ opencl? ( virtual/opencl ) |
87 |
+ fftw? ( sci-libs/fftw:3.0 ) |
88 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
89 |
+ lapack? ( virtual/lapack ) |
90 |
+ mkl? ( sci-libs/mkl ) |
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+ mpi? ( virtual/mpi ) |
92 |
+ " |
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+DEPEND="${CDEPEND} |
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+ virtual/pkgconfig |
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+ doc? ( |
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+ app-doc/doxygen |
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+ dev-texlive/texlive-latex |
98 |
+ dev-texlive/texlive-latexextra |
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+ media-gfx/imagemagick |
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+ )" |
101 |
+RDEPEND="${CDEPEND}" |
102 |
+ |
103 |
+REQUIRED_USE=" |
104 |
+ || ( single-precision double-precision ) |
105 |
+ cuda? ( single-precision ) |
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+ cuda? ( !opencl ) |
107 |
+ mkl? ( !blas !fftw !lapack )" |
108 |
+ |
109 |
+DOCS=( AUTHORS README ) |
110 |
+ |
111 |
+if [[ ${PV} != *9999 ]]; then |
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+ S="${WORKDIR}/${PN}-${PV/_/-}" |
113 |
+fi |
114 |
+ |
115 |
+pkg_pretend() { |
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+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
117 |
+ use openmp && ! tc-has-openmp && \ |
118 |
+ die "Please switch to an openmp compatible compiler" |
119 |
+} |
120 |
+ |
121 |
+src_unpack() { |
122 |
+ if [[ ${PV} != *9999 ]]; then |
123 |
+ default |
124 |
+ else |
125 |
+ git-r3_src_unpack |
126 |
+ if use test; then |
127 |
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
128 |
+ EGIT_BRANCH="${EGIT_BRANCH}" \ |
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+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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+ git-r3_src_unpack |
131 |
+ fi |
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+ fi |
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+} |
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+ |
135 |
+src_prepare() { |
136 |
+ #notes/todos |
137 |
+ # -on apple: there is framework support |
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+ |
139 |
+ xdg_environment_reset #591952 |
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+ |
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+ cmake-utils_src_prepare |
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+ |
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+ use cuda && cuda_src_prepare |
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+ |
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+ GMX_DIRS="" |
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+ use single-precision && GMX_DIRS+=" float" |
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+ use double-precision && GMX_DIRS+=" double" |
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+ |
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+ if use test; then |
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+ for x in ${GMX_DIRS}; do |
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+ mkdir -p "${WORKDIR}/${P}_${x}" || die |
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+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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+ done |
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+ fi |
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+ |
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+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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+} |
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+ |
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+src_configure() { |
160 |
+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
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+ |
162 |
+ #go from slowest to fastest acceleration |
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+ local acce="None" |
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+ use cpu_flags_x86_sse2 && acce="SSE2" |
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+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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+ use cpu_flags_x86_avx && acce="AVX_256" |
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+ use cpu_flags_x86_avx2 && acce="AVX2_256" |
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+ |
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+ #to create man pages, build tree binaries are executed (bug #398437) |
171 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
172 |
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
173 |
+ |
174 |
+ if use fftw; then |
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+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
177 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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+ ) |
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+ elif use mkl; then |
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+ local bits=$(get_libdir) |
183 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
186 |
+ ) |
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+ else |
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+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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+ fi |
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+ |
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+ mycmakeargs_pre+=( |
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+ "${fft_opts[@]}" |
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+ -DGMX_X11=$(usex X) |
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+ -DGMX_EXTERNAL_BLAS=$(usex blas) |
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+ -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
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+ -DGMX_OPENMP=$(usex openmp) |
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+ -DGMX_COOL_QUOTES=$(usex offensive) |
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+ -DGMX_USE_TNG=$(usex tng) |
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+ -DGMX_BUILD_MANUAL=$(usex doc) |
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+ -DGMX_HWLOC=$(usex hwloc) |
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+ -DGMX_DEFAULT_SUFFIX=off |
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+ -DGMX_SIMD="$acce" |
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+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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+ -DBUILD_TESTING=$(usex test) |
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+ -DGMX_BUILD_UNITTESTS=$(usex test) |
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+ ${extra} |
207 |
+ ) |
208 |
+ |
209 |
+ for x in ${GMX_DIRS}; do |
210 |
+ einfo "Configuring for ${x} precision" |
211 |
+ local suffix="" |
212 |
+ #if we build single and double - double is suffixed |
213 |
+ use double-precision && use single-precision && \ |
214 |
+ [[ ${x} = "double" ]] && suffix="_d" |
215 |
+ local p |
216 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
217 |
+ local cuda=( "-DGMX_GPU=OFF" ) |
218 |
+ [[ ${x} = "float" ]] && use cuda && \ |
219 |
+ cuda=( "-DGMX_GPU=ON" ) |
220 |
+ local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
221 |
+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
222 |
+ mycmakeargs=( |
223 |
+ ${mycmakeargs_pre[@]} ${p} |
224 |
+ -DGMX_MPI=OFF |
225 |
+ -DGMX_THREAD_MPI=$(usex threads) |
226 |
+ "${opencl[@]}" |
227 |
+ "${cuda[@]}" |
228 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
229 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
230 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
231 |
+ ) |
232 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
233 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
234 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
235 |
+ use mpi || continue |
236 |
+ einfo "Configuring for ${x} precision with mpi" |
237 |
+ mycmakeargs=( |
238 |
+ ${mycmakeargs_pre[@]} ${p} |
239 |
+ -DGMX_THREAD_MPI=OFF |
240 |
+ -DGMX_MPI=ON ${cuda} |
241 |
+ -DGMX_OPENMM=OFF |
242 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
243 |
+ -DBUILD_SHARED_LIBS=OFF |
244 |
+ -DGMX_BUILD_MANUAL=OFF |
245 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
246 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
247 |
+ ) |
248 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
249 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
250 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
251 |
+ done |
252 |
+} |
253 |
+ |
254 |
+src_compile() { |
255 |
+ for x in ${GMX_DIRS}; do |
256 |
+ einfo "Compiling for ${x} precision" |
257 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
258 |
+ cmake-utils_src_compile |
259 |
+ # not 100% necessary for rel ebuilds as available from website |
260 |
+ if use doc; then |
261 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
262 |
+ cmake-utils_src_compile manual |
263 |
+ fi |
264 |
+ use mpi || continue |
265 |
+ einfo "Compiling for ${x} precision with mpi" |
266 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
267 |
+ cmake-utils_src_compile |
268 |
+ done |
269 |
+} |
270 |
+ |
271 |
+src_test() { |
272 |
+ for x in ${GMX_DIRS}; do |
273 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
274 |
+ cmake-utils_src_make check |
275 |
+ done |
276 |
+} |
277 |
+ |
278 |
+src_install() { |
279 |
+ for x in ${GMX_DIRS}; do |
280 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
281 |
+ cmake-utils_src_install |
282 |
+ if use doc; then |
283 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
284 |
+ fi |
285 |
+ use mpi || continue |
286 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
287 |
+ cmake-utils_src_install |
288 |
+ done |
289 |
+ |
290 |
+ if use tng; then |
291 |
+ insinto /usr/include/tng |
292 |
+ doins src/external/tng_io/include/tng/*h |
293 |
+ fi |
294 |
+ # drop unneeded stuff |
295 |
+ rm "${ED}"usr/bin/GMXRC* || die |
296 |
+ for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
297 |
+ local n=${x##*/gmx-completion-} |
298 |
+ n="${n%.bash}" |
299 |
+ cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
300 |
+ newbashcomp "${T}"/"${n}" "${n}" |
301 |
+ done |
302 |
+ rm "${ED}"usr/bin/gmx-completion*.bash || die |
303 |
+ readme.gentoo_create_doc |
304 |
+} |
305 |
+ |
306 |
+pkg_postinst() { |
307 |
+ einfo |
308 |
+ einfo "Please read and cite:" |
309 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
310 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
311 |
+ einfo |
312 |
+ readme.gentoo_print_elog |
313 |
+} |
314 |
|
315 |
diff --git a/sci-chemistry/gromacs/gromacs-2018.4.ebuild b/sci-chemistry/gromacs/gromacs-2018.4.ebuild |
316 |
new file mode 100644 |
317 |
index 00000000000..485db2a26ac |
318 |
--- /dev/null |
319 |
+++ b/sci-chemistry/gromacs/gromacs-2018.4.ebuild |
320 |
@@ -0,0 +1,270 @@ |
321 |
+# Copyright 1999-2018 Gentoo Authors |
322 |
+# Distributed under the terms of the GNU General Public License v2 |
323 |
+ |
324 |
+EAPI=6 |
325 |
+ |
326 |
+CMAKE_MAKEFILE_GENERATOR="ninja" |
327 |
+ |
328 |
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
329 |
+ |
330 |
+if [[ $PV = *9999* ]]; then |
331 |
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
332 |
+ https://gerrit.gromacs.org/gromacs.git |
333 |
+ https://github.com/gromacs/gromacs.git |
334 |
+ http://repo.or.cz/r/gromacs.git" |
335 |
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
336 |
+ inherit git-r3 |
337 |
+else |
338 |
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
339 |
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
340 |
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
341 |
+fi |
342 |
+ |
343 |
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
344 |
+ |
345 |
+DESCRIPTION="The ultimate molecular dynamics simulation package" |
346 |
+HOMEPAGE="http://www.gromacs.org/" |
347 |
+ |
348 |
+# see COPYING for details |
349 |
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
350 |
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
351 |
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
352 |
+SLOT="0/${PV}" |
353 |
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
354 |
+ |
355 |
+CDEPEND=" |
356 |
+ X? ( |
357 |
+ x11-libs/libX11 |
358 |
+ x11-libs/libSM |
359 |
+ x11-libs/libICE |
360 |
+ ) |
361 |
+ blas? ( virtual/blas ) |
362 |
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
363 |
+ opencl? ( virtual/opencl ) |
364 |
+ fftw? ( sci-libs/fftw:3.0 ) |
365 |
+ hwloc? ( <sys-apps/hwloc-2 ) |
366 |
+ lapack? ( virtual/lapack ) |
367 |
+ mkl? ( sci-libs/mkl ) |
368 |
+ mpi? ( virtual/mpi ) |
369 |
+ " |
370 |
+DEPEND="${CDEPEND} |
371 |
+ virtual/pkgconfig |
372 |
+ doc? ( |
373 |
+ app-doc/doxygen |
374 |
+ dev-texlive/texlive-latex |
375 |
+ dev-texlive/texlive-latexextra |
376 |
+ media-gfx/imagemagick |
377 |
+ )" |
378 |
+RDEPEND="${CDEPEND}" |
379 |
+ |
380 |
+REQUIRED_USE=" |
381 |
+ || ( single-precision double-precision ) |
382 |
+ cuda? ( single-precision ) |
383 |
+ cuda? ( !opencl ) |
384 |
+ mkl? ( !blas !fftw !lapack )" |
385 |
+ |
386 |
+DOCS=( AUTHORS README ) |
387 |
+ |
388 |
+if [[ ${PV} != *9999 ]]; then |
389 |
+ S="${WORKDIR}/${PN}-${PV/_/-}" |
390 |
+fi |
391 |
+ |
392 |
+pkg_pretend() { |
393 |
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
394 |
+ use openmp && ! tc-has-openmp && \ |
395 |
+ die "Please switch to an openmp compatible compiler" |
396 |
+} |
397 |
+ |
398 |
+src_unpack() { |
399 |
+ if [[ ${PV} != *9999 ]]; then |
400 |
+ default |
401 |
+ else |
402 |
+ git-r3_src_unpack |
403 |
+ if use test; then |
404 |
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
405 |
+ EGIT_BRANCH="${EGIT_BRANCH}" \ |
406 |
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
407 |
+ git-r3_src_unpack |
408 |
+ fi |
409 |
+ fi |
410 |
+} |
411 |
+ |
412 |
+src_prepare() { |
413 |
+ #notes/todos |
414 |
+ # -on apple: there is framework support |
415 |
+ |
416 |
+ xdg_environment_reset #591952 |
417 |
+ |
418 |
+ cmake-utils_src_prepare |
419 |
+ |
420 |
+ use cuda && cuda_src_prepare |
421 |
+ |
422 |
+ GMX_DIRS="" |
423 |
+ use single-precision && GMX_DIRS+=" float" |
424 |
+ use double-precision && GMX_DIRS+=" double" |
425 |
+ |
426 |
+ if use test; then |
427 |
+ for x in ${GMX_DIRS}; do |
428 |
+ mkdir -p "${WORKDIR}/${P}_${x}" || die |
429 |
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
430 |
+ done |
431 |
+ fi |
432 |
+ |
433 |
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
434 |
+} |
435 |
+ |
436 |
+src_configure() { |
437 |
+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
438 |
+ |
439 |
+ #go from slowest to fastest acceleration |
440 |
+ local acce="None" |
441 |
+ use cpu_flags_x86_sse2 && acce="SSE2" |
442 |
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
443 |
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
444 |
+ use cpu_flags_x86_avx && acce="AVX_256" |
445 |
+ use cpu_flags_x86_avx2 && acce="AVX2_256" |
446 |
+ |
447 |
+ #to create man pages, build tree binaries are executed (bug #398437) |
448 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
449 |
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
450 |
+ |
451 |
+ if use fftw; then |
452 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
453 |
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
454 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
455 |
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
456 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
457 |
+ ) |
458 |
+ elif use mkl; then |
459 |
+ local bits=$(get_libdir) |
460 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
461 |
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
462 |
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
463 |
+ ) |
464 |
+ else |
465 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
466 |
+ fi |
467 |
+ |
468 |
+ mycmakeargs_pre+=( |
469 |
+ "${fft_opts[@]}" |
470 |
+ -DGMX_X11=$(usex X) |
471 |
+ -DGMX_EXTERNAL_BLAS=$(usex blas) |
472 |
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
473 |
+ -DGMX_OPENMP=$(usex openmp) |
474 |
+ -DGMX_COOL_QUOTES=$(usex offensive) |
475 |
+ -DGMX_USE_TNG=$(usex tng) |
476 |
+ -DGMX_BUILD_MANUAL=$(usex doc) |
477 |
+ -DGMX_HWLOC=$(usex hwloc) |
478 |
+ -DGMX_DEFAULT_SUFFIX=off |
479 |
+ -DGMX_SIMD="$acce" |
480 |
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
481 |
+ -DBUILD_TESTING=$(usex test) |
482 |
+ -DGMX_BUILD_UNITTESTS=$(usex test) |
483 |
+ ${extra} |
484 |
+ ) |
485 |
+ |
486 |
+ for x in ${GMX_DIRS}; do |
487 |
+ einfo "Configuring for ${x} precision" |
488 |
+ local suffix="" |
489 |
+ #if we build single and double - double is suffixed |
490 |
+ use double-precision && use single-precision && \ |
491 |
+ [[ ${x} = "double" ]] && suffix="_d" |
492 |
+ local p |
493 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
494 |
+ local cuda=( "-DGMX_GPU=OFF" ) |
495 |
+ [[ ${x} = "float" ]] && use cuda && \ |
496 |
+ cuda=( "-DGMX_GPU=ON" ) |
497 |
+ local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
498 |
+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
499 |
+ mycmakeargs=( |
500 |
+ ${mycmakeargs_pre[@]} ${p} |
501 |
+ -DGMX_MPI=OFF |
502 |
+ -DGMX_THREAD_MPI=$(usex threads) |
503 |
+ "${opencl[@]}" |
504 |
+ "${cuda[@]}" |
505 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
506 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
507 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
508 |
+ ) |
509 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
510 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
511 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
512 |
+ use mpi || continue |
513 |
+ einfo "Configuring for ${x} precision with mpi" |
514 |
+ mycmakeargs=( |
515 |
+ ${mycmakeargs_pre[@]} ${p} |
516 |
+ -DGMX_THREAD_MPI=OFF |
517 |
+ -DGMX_MPI=ON ${cuda} |
518 |
+ -DGMX_OPENMM=OFF |
519 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
520 |
+ -DBUILD_SHARED_LIBS=OFF |
521 |
+ -DGMX_BUILD_MANUAL=OFF |
522 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
523 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
524 |
+ ) |
525 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
526 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
527 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
528 |
+ done |
529 |
+} |
530 |
+ |
531 |
+src_compile() { |
532 |
+ for x in ${GMX_DIRS}; do |
533 |
+ einfo "Compiling for ${x} precision" |
534 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
535 |
+ cmake-utils_src_compile |
536 |
+ # not 100% necessary for rel ebuilds as available from website |
537 |
+ if use doc; then |
538 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
539 |
+ cmake-utils_src_compile manual |
540 |
+ fi |
541 |
+ use mpi || continue |
542 |
+ einfo "Compiling for ${x} precision with mpi" |
543 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
544 |
+ cmake-utils_src_compile |
545 |
+ done |
546 |
+} |
547 |
+ |
548 |
+src_test() { |
549 |
+ for x in ${GMX_DIRS}; do |
550 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
551 |
+ cmake-utils_src_make check |
552 |
+ done |
553 |
+} |
554 |
+ |
555 |
+src_install() { |
556 |
+ for x in ${GMX_DIRS}; do |
557 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
558 |
+ cmake-utils_src_install |
559 |
+ if use doc; then |
560 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
561 |
+ fi |
562 |
+ use mpi || continue |
563 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
564 |
+ cmake-utils_src_install |
565 |
+ done |
566 |
+ |
567 |
+ if use tng; then |
568 |
+ insinto /usr/include/tng |
569 |
+ doins src/external/tng_io/include/tng/*h |
570 |
+ fi |
571 |
+ # drop unneeded stuff |
572 |
+ rm "${ED}"usr/bin/GMXRC* || die |
573 |
+ for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
574 |
+ local n=${x##*/gmx-completion-} |
575 |
+ n="${n%.bash}" |
576 |
+ cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
577 |
+ newbashcomp "${T}"/"${n}" "${n}" |
578 |
+ done |
579 |
+ rm "${ED}"usr/bin/gmx-completion*.bash || die |
580 |
+ readme.gentoo_create_doc |
581 |
+} |
582 |
+ |
583 |
+pkg_postinst() { |
584 |
+ einfo |
585 |
+ einfo "Please read and cite:" |
586 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
587 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
588 |
+ einfo |
589 |
+ readme.gentoo_print_elog |
590 |
+} |